Factors affecting the STR amplification success in poorly preserved bone samples

Area of Science:

• Forensic Science
• Molecular Biology
• Genetics

Background:

• Systematic assessment of factors influencing short tandem repeat (STR) amplification in poorly preserved samples is limited.
• Understanding these factors is crucial for successful DNA profiling from challenging sources like old bones.

Purpose of the Study:

• To systematically assess the relative importance of DNA quantity, degradation, and inhibition on STR genotyping success.
• To evaluate error rates such as allelic drop-out and drop-in in STR analyses.

Main Methods:

• Utilized two maximum likelihood-based methods for analysis.
• Employed a generalized linear mixed model to estimate the effects of PCR amplification factors.
• Estimated error rates based on mismatches between replicates.

Main Results:

• DNA quantity was the most critical factor in autosomal STR analysis, followed by degradation.
• DNA degradation was the primary factor in Y-chromosomal STR analysis.
• Inhibition played a minor role in STR analyses of poorly preserved bones.

Conclusions:

• PCR amplification success is largely dependent on template DNA quality (amount and degradation).
• Primer design and amplification chemistry can partially mitigate issues related to DNA quality.
• The relative impact of compromising factors varies depending on the specific STR kit utilized.